13
Transcriptome Responses
of Spirodela polyrhiza
Paul Fourounjian
Abstract
In order to analyze the transcriptome of any
species, RNA-seq has become the gold standard and evolved into a variety of library
preparations and sequencing platforms to
study more than mRNA abundance. This
chapter reviews the transcriptional studies of
Spirodela polyrhiza, the best-characterized
member of the Lemnaceae family in a
genomic sense. To date, there have been three
studies of its transcriptome. The first two
analyzed ribosomal RNA depleted total RNA
of fronds and fronds developing into turions
after exposure to abscisic acid. The first study
analyzed 154 down-regulated genes involved
in growth and 208 upregulated genes involved
in starch, anthocyanin production, and seed
development. The second study found 66 sites
where chloroplast mRNAs were edited to
create a functional protein, supporting the
hypothesis that mRNA editing was evolved
once, and the conservation of editing sites was
phylogenetically correlated. The third study,
also performed in the 7498 ecotypes, was
sequencing of the uncapped polyadenylated
transcripts. While the main aim was to
observe miRNA induced cleavage, differences
in the post-transcriptional regulation or abundance of degraded transcripts across the eight
sequencing conditions can be observed. Taken
together, these studies cover mRNA expression, post-transcriptional editing, and finally
degradation.
Scientists have been interested in gene expression ever since discovering the central dogma of
biology and have developed a number of methods over the decades to measure RNA quantity.
After reverse transcription was discovered in
1970, Northern blot and Sanger sequencing
followed in 1977, qPCR came out in the late
1980s, and then in 2005, the Roche 454
sequencing platform applied shotgun genome
sequencing technology to massively parallel
RNA-sequencing and quantification (Cieślik and
Chinnaiyan 2017). The data from these Roche
and Illumina sequencers were typically thousands to millions of 50–200 nt reads that need to
be mapped to the genome and reassembled to
determine splicing patterns and gene expression
as fragments per kilobase per million (FPKM).
Joining the next-generation sequencers are the
high throughput, long-read sequencers like PacBio and Oxford Nanopore systems available in
2011 which often produce 20–200 kB reads that
can easily span entire mRNA and long
non-coding RNA transcripts (1–2 kb), thereby
eliminating the reassembly steps to more precisely map the transcriptome with its splicing
patterns and alternative polyadenylation sites.
Unfortunately, the present challenge with these
P. Fourounjian (&)
Waksman Institute of Microbiology, Rutgers
University, Piscataway 08854, USA
e-mail: pjf99@scarletmail.rutgers.edu
© Springer Nature Switzerland AG 2020
X. H. Cao et al. (eds.), The Duckweed Genomes, Compendium of Plant Genomes,
https://doi.org/10.1007/978-3-030-11045-1_13
133
Transcriptome Responses
of Spirodela polyrhiza
Paul Fourounjian
Abstract
In order to analyze the transcriptome of any
species, RNA-seq has become the gold standard and evolved into a variety of library
preparations and sequencing platforms to
study more than mRNA abundance. This
chapter reviews the transcriptional studies of
Spirodela polyrhiza, the best-characterized
member of the Lemnaceae family in a
genomic sense. To date, there have been three
studies of its transcriptome. The first two
analyzed ribosomal RNA depleted total RNA
of fronds and fronds developing into turions
after exposure to abscisic acid. The first study
analyzed 154 down-regulated genes involved
in growth and 208 upregulated genes involved
in starch, anthocyanin production, and seed
development. The second study found 66 sites
where chloroplast mRNAs were edited to
create a functional protein, supporting the
hypothesis that mRNA editing was evolved
once, and the conservation of editing sites was
phylogenetically correlated. The third study,
also performed in the 7498 ecotypes, was
sequencing of the uncapped polyadenylated
transcripts. While the main aim was to
observe miRNA induced cleavage, differences
in the post-transcriptional regulation or abundance of degraded transcripts across the eight
sequencing conditions can be observed. Taken
together, these studies cover mRNA expression, post-transcriptional editing, and finally
degradation.
Scientists have been interested in gene expression ever since discovering the central dogma of
biology and have developed a number of methods over the decades to measure RNA quantity.
After reverse transcription was discovered in
1970, Northern blot and Sanger sequencing
followed in 1977, qPCR came out in the late
1980s, and then in 2005, the Roche 454
sequencing platform applied shotgun genome
sequencing technology to massively parallel
RNA-sequencing and quantification (Cieślik and
Chinnaiyan 2017). The data from these Roche
and Illumina sequencers were typically thousands to millions of 50–200 nt reads that need to
be mapped to the genome and reassembled to
determine splicing patterns and gene expression
as fragments per kilobase per million (FPKM).
Joining the next-generation sequencers are the
high throughput, long-read sequencers like PacBio and Oxford Nanopore systems available in
2011 which often produce 20–200 kB reads that
can easily span entire mRNA and long
non-coding RNA transcripts (1–2 kb), thereby
eliminating the reassembly steps to more precisely map the transcriptome with its splicing
patterns and alternative polyadenylation sites.
Unfortunately, the present challenge with these
P. Fourounjian (&)
Waksman Institute of Microbiology, Rutgers
University, Piscataway 08854, USA
e-mail: pjf99@scarletmail.rutgers.edu
© Springer Nature Switzerland AG 2020
X. H. Cao et al. (eds.), The Duckweed Genomes, Compendium of Plant Genomes,
https://doi.org/10.1007/978-3-030-11045-1_13
133